[med-svn] [SCM] tabix branch, master, updated. debian/0.2.5-1-13-g84d11c8

[Andreas Tille]

The following commit has been merged in the master branch:
commit 6d477f08c26b45742a1693e22fd59e24b8fa5e8d
Author: Andreas Tille <tille at debian.org>
Date:   Sat May 12 08:38:37 2012 +0200

    Really enable hardening flags

diff --git a/debian/changelog b/debian/changelog
index caa61b5..f788d41 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,9 @@ tabix (0.2.5-3) UNRELEASED; urgency=low
   * debian/patches/ld-as-needed.patch:  Enable building with --as-needed
     (Thanks to David Shorten <dpshorten at gmail.com> for the patch)
     Closes: #632150
+  * debian/patches/use-dpkg-buildflags.patch: Really enable hardening
+    build flags (Thanks for the patch to Simon Ruderich <simon at ruderich.org>)
+    Closes: #670759
 
  -- Andreas Tille <tille at debian.org>  Fri, 11 May 2012 13:32:56 +0200
 
diff --git a/debian/patches/use-dpkg-buildflags.patch b/debian/patches/use-dpkg-buildflags.patch
index 7856be7..7ece66b 100644
--- a/debian/patches/use-dpkg-buildflags.patch
+++ b/debian/patches/use-dpkg-buildflags.patch
@@ -1,11 +1,49 @@
+Author: Simon Ruderich <simon at ruderich.org>
+Date: Sat, 28 Apr 2012 19:09:02 UTC
+Description: Fix build system to enable hardening flags
+
 --- tabix.orig/Makefile
 +++ tabix/Makefile
-@@ -12,7 +12,7 @@
+@@ -1,5 +1,8 @@
+ CC=			gcc
+-CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-arch ppc
++# Use flags when CFLAGS is not already defined in the environment.
++CFLAGS?=		-g -Wall -O2
++# But always append special flags we need.
++CFLAGS+= -fPIC #-m64 #-arch ppc
+ DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ LOBJS=		bgzf.o kstring.o knetfile.o index.o bedidx.o
+ AOBJS=		main.o
+@@ -12,7 +15,7 @@
  .SUFFIXES:.c .o
  
  .c.o:
 -		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+		$(CC) -c $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(DFLAGS) $(LDFLAGS) $(INCLUDES) $< -o $@
++		$(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
  
  all-recur lib-recur clean-recur cleanlocal-recur install-recur:
  		@target=`echo $@ | sed s/-recur//`; \
+@@ -29,19 +32,19 @@
+ lib:libtabix.a
+ 
+ libtabix.so.1:$(LOBJS)
+-		$(CC) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
+ 
+ libtabix.1.dylib:$(LOBJS)
+-		libtool -dynamic $(LOBJS) -o $@ -lc -lz
++		libtool $(CFLAGS) $(LDFLAGS) -dynamic $(LOBJS) -o $@ -lc -lz
+ 
+ libtabix.a:$(LOBJS)
+ 		$(AR) -cru $@ $(LOBJS)
+ 
+ tabix:lib $(AOBJS)
+-		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
+ 
+ bgzip:bgzip.o bgzf.o knetfile.o
+-		$(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
+ 
+ TabixReader.class:TabixReader.java
+ 		javac -cp .:sam.jar TabixReader.java

-- 
Generic indexer for TAB-delimited genome position files.